LAMMPS (3 Aug 2023 - Development - patch_2Aug2023-790-g0fbe388cbd)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task
# 2d circle of particles inside a box with LJ walls

variable        b index 0

variable        x index 50
variable        y index 20
variable        d index 20
variable        v index 5
variable        w index 2

units           lj
dimension       2
atom_style      bond
boundary        f f p

lattice         hex 0.85
Lattice spacing in x,y,z = 1.1655347 2.0187654 1.1655347
region          box block 0 $x 0 $y -0.5 0.5
region          box block 0 50 0 $y -0.5 0.5
region          box block 0 50 0 20 -0.5 0.5
create_box      1 box bond/types 1 extra/bond/per/atom 6
Created orthogonal box = (0 0 -0.58276737) to (58.276737 40.375308 0.58276737)
  2 by 1 by 1 MPI processor grid
region          circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region          circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region          circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
region          circle sphere 11 6.7735026918962581988 0.0 10
create_atoms    1 region circle
Created 361 atoms
  using lattice units in orthogonal box = (0 0 -0.58276737) to (58.276737 40.375308 0.58276737)
  create_atoms CPU = 0.001 seconds
mass            1 1.0

velocity        all create 0.5 87287 loop geom
velocity        all set $v $w 0 sum yes
velocity        all set 5 $w 0 sum yes
velocity        all set 5 2 0 sum yes

pair_style      lj/cut 2.5
pair_coeff      1 1 10.0 1.0 2.5

bond_style      harmonic
bond_coeff      1 10.0 1.2

# need to preserve 1-3, 1-4 pairwise interactions during hard collisions

special_bonds   lj/coul 0 1 1
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        1        1       
  special bond factors coul:  0        1        1       
     0 = max # of 1-2 neighbors
     1 = max # of special neighbors
  special bonds CPU = 0.000 seconds
create_bonds    many all all 1 1.0 1.5
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.8
  ghost atom cutoff = 2.8
  binsize = 1.4, bins = 42 29 1
  2 neighbor lists, perpetual/occasional/extra = 1 1 0
  (1) command create_bonds, occasional
      attributes: full, newton on
      pair build: full/bin
      stencil: full/bin/2d
      bin: standard
  (2) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/2d
      bin: standard
Added 1014 bonds, new total = 1014
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        1        1       
  special bond factors coul:  0        1        1       
     6 = max # of 1-2 neighbors
     6 = max # of special neighbors
  special bonds CPU = 0.000 seconds

neighbor        0.3 bin
neigh_modify    delay 0 every 1 check yes

fix             1 all nve

fix             2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
fix             2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
fix             3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
fix             3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5

comm_style      tiled
comm_modify     cutoff 10.0   # because bonds stretch a long ways
fix             10 all balance 50 0.9 rcb

#compute         1 all property/atom proc
#variable        p atom (c_1%10)+1
#dump            2 all custom 50 tmp.dump id v_p x y z

#dump            3 all image 50 image.*.jpg v_p type bond atom 0.25 #                adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
#variable        colors string #                "red green blue yellow white #                purple pink orange lime gray"
#dump_modify     3 pad 5 amap 0 10 sa 1 10 ${colors}

thermo_style    custom step temp epair press f_10[3] f_10
thermo          100
timestep        0.001

run             10000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.8
  ghost atom cutoff = 10
  binsize = 1.4, bins = 42 29 1
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/2d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.157 | 5.167 | 5.178 Mbytes
   Step          Temp          E_pair         Press         f_10[3]          f_10     
         0   25.701528     -2.2032569      3.1039469      2              1.0193906    
       100   25.57187      -2.2902218      2.9990153      1.0193906      1.0027701    
       200   25.532511     -2.5273097      2.8286231      1.0304709      1.0027701    
       300   25.860246     -3.0674998      2.6725358      1.0138504      1.0027701    
       400   26.628011     -4.394738       2.6618897      1.0138504      1.0083102    
       500   27.627309     -6.2305012      2.6564278      1.0138504      1.0027701    
       600   28.881803     -8.2757766      2.8249236      1.0138504      1.0027701    
       700   29.941402     -9.9816088      2.9828232      1.0138504      1.0027701    
       800   31.118457     -12.199787      3.2044549      1.0249307      1.0083102    
       900   32.393498     -14.204491      2.9496587      1.0304709      1.0027701    
      1000   33.392657     -15.747519      3.1613807      1.0249307      1.0027701    
      1100   34.671769     -17.728904      3.019138       1.0193906      1.0083102    
      1200   35.632627     -19.846347      3.1061176      1.0193906      1.0083102    
      1300   36.77272      -21.156179      3.2353009      1.0415512      1.0027701    
      1400   38.241608     -22.744765      4.1163075      1.0193906      1.0027701    
      1500   40.072478     -25.139827      5.3032535      1.0304709      1.0027701    
      1600   40.665382     -25.901697      5.4330761      1.0304709      1.0027701    
      1700   40.957034     -26.28667       7.1881521      1.0360111      1.0027701    
      1800   41.536831     -27.393841      6.6814405      1.0470914      1.0027701    
      1900   41.952676     -28.123051      7.4683871      1.0360111      1.0027701    
      2000   42.201937     -28.685743      7.4624285      1.0304709      1.0027701    
      2100   41.509082     -27.909225      6.8666951      1.0304709      1.0083102    
      2200   40.794911     -27.085519      5.2599455      1.0415512      1.0027701    
      2300   38.74971      -25.146012      4.2936194      1.0360111      1.0083102    
      2400   38.418073     -24.593601      3.1418121      1.0470914      1.0027701    
      2500   36.932581     -23.407617      1.9397617      1.0304709      1.0027701    
      2600   35.979152     -23.066707      2.1676871      1.0415512      1.0027701    
      2700   35.848339     -22.556586      2.079815       1.0526316      1.0027701    
      2800   35.796197     -22.092919      2.6843042      1.0470914      1.0027701    
      2900   35.752758     -21.6603        2.4924275      1.0360111      1.0083102    
      3000   36.548479     -21.940002      2.8478206      1.0304709      1.0027701    
      3100   36.74473      -22.072441      3.7028736      1.0193906      1.0027701    
      3200   36.633543     -22.568923      3.7319143      1.0249307      1.0083102    
      3300   37.175051     -23.069268      3.5045201      1.0193906      1.0027701    
      3400   36.942892     -23.480254      3.1212991      1.0193906      1.0027701    
      3500   37.813564     -24.659011      3.6045332      1.0138504      1.0027701    
      3600   37.856787     -24.954353      4.3062815      1.0249307      1.0027701    
      3700   38.543481     -25.054481      4.7177629      1.0304709      1.0027701    
      3800   39.011196     -25.760455      4.9664492      1.0304709      1.0027701    
      3900   38.784228     -25.618896      4.944851       1.0304709      1.0027701    
      4000   39.348833     -26.615389      4.8191233      1.0304709      1.0027701    
      4100   39.242191     -26.754066      4.7960336      1.0249307      1.0027701    
      4200   38.989902     -26.741978      3.7980048      1.0415512      1.0027701    
      4300   38.726515     -25.916493      3.7176038      1.0304709      1.0027701    
      4400   38.720441     -25.549542      3.3956415      1.0470914      1.0027701    
      4500   38.22257      -25.122141      4.5771547      1.0304709      1.0083102    
      4600   38.217511     -25.390842      4.4896706      1.0360111      1.0027701    
      4700   39.121636     -26.227786      4.9811267      1.0415512      1.0083102    
      4800   39.306166     -26.700977      4.9963051      1.0249307      1.0027701    
      4900   38.909059     -25.799524      6.1957543      1.0692521      1.0027701    
      5000   38.778196     -26.491002      5.6393984      1.0526316      1.0027701    
      5100   38.587868     -27.253335      5.5460314      1.0415512      1.0027701    
      5200   38.686438     -27.40612       5.5186442      1.0249307      1.0027701    
      5300   37.986414     -26.049806      5.3696903      1.0304709      1.0027701    
      5400   37.111804     -26.019738      4.2114526      1.0415512      1.0083102    
      5500   36.62295      -25.592884      5.1349         1.0415512      1.0027701    
      5600   36.087987     -25.398454      4.4963434      1.0249307      1.0083102    
      5700   34.435409     -24.548062      3.5310124      1.0249307      1.0027701    
      5800   33.18681      -22.76355       3.2061242      1.0470914      1.0027701    
      5900   32.57428      -21.832024      3.2865828      1.0193906      1.0027701    
      6000   30.557555     -20.714816      4.2280358      1.0304709      1.0083102    
      6100   31.893092     -21.235479      4.5931729      1.0304709      1.0027701    
      6200   31.577761     -21.222778      4.1847871      1.0415512      1.0027701    
      6300   32.003743     -20.825156      5.6968257      1.0526316      1.0027701    
      6400   32.073012     -20.877815      7.3062956      1.0360111      1.0027701    
      6500   31.588306     -21.556202      5.7846536      1.0138504      1.0027701    
      6600   32.453985     -21.478064      4.8089249      1.0083102      1.0027701    
      6700   31.269576     -21.24005       4.0540095      1.0193906      1.0027701    
      6800   31.548438     -21.335039      3.767158       1.0138504      1.0027701    
      6900   31.249216     -20.689547      4.5435057      1.0083102      1.0027701    
      7000   31.72893      -20.373971      6.0204212      1.0249307      1.0027701    
      7100   30.888569     -19.028984      5.2458824      1.0027701      1.0027701    
      7200   30.747229     -19.579694      3.2582453      1.0138504      1.0083102    
      7300   28.339584     -19.225504      3.1235472      1.0193906      1.0027701    
      7400   26.754307     -18.557545      1.3860606      1.0193906      1.0083102    
      7500   26.559389     -17.395026      1.7206081      1.0138504      1.0083102    
      7600   26.227728     -16.755138      2.1148459      1.0193906      1.0027701    
      7700   26.361463     -15.711397      2.5458994      1.0138504      1.0027701    
      7800   26.081484     -16.032712      0.70050048     1.0138504      1.0027701    
      7900   24.660082     -15.079215      1.1999533      1.0138504      1.0027701    
      8000   24.448184     -14.668849      0.63886653     1.0138504      1.0083102    
      8100   24.198589     -15.157555      0.12256041     1.0027701      1.0027701    
      8200   24.764129     -14.876966      0.97060609     1.0249307      1.0083102    
      8300   25.33268      -14.891698      1.6089548      1.0083102      1.0027701    
      8400   24.992342     -14.652659      1.3317376      1.0138504      1.0027701    
      8500   25.115045     -14.683247      0.98361969     1.0138504      1.0027701    
      8600   24.954894     -14.451543      1.2228755      1.0083102      1.0027701    
      8700   24.51303      -14.159235      0.75345783     1.0249307      1.0083102    
      8800   22.697326     -13.254743      1.2913804      1.0138504      1.0027701    
      8900   22.868775     -13.677092     -0.048154854    1.0083102      1.0027701    
      9000   25.269332     -13.649225      1.0337367      1.0083102      1.0083102    
      9100   24.184813     -12.826606      1.1160895      1.0360111      1.0027701    
      9200   23.664589     -13.449013      0.031451624    1.0193906      1.0083102    
      9300   23.944566     -13.401803      0.20095909     1.0193906      1.0027701    
      9400   24.146696     -12.879011      0.89518549     1.0249307      1.0027701    
      9500   25.383214     -13.411768      0.95798595     1.0304709      1.0027701    
      9600   25.248933     -13.838658      0.45253554     1.0304709      1.0027701    
      9700   24.38613      -13.123006      1.5446061      1.0138504      1.0027701    
      9800   25.743921     -13.610838      1.2556191      1.0083102      1.0027701    
      9900   26.468479     -13.72971       2.3998562      1.0249307      1.0027701    
     10000   26.338099     -14.82183       1.5233934      1.0193906      1.0027701    
Loop time of 0.372607 on 2 procs for 10000 steps with 361 atoms

Performance: 2318795.909 tau/day, 26837.916 timesteps/s, 9.688 Matom-step/s
96.0% CPU use with 2 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.13582    | 0.14029    | 0.14475    |   1.2 | 37.65
Bond    | 0.035027   | 0.035038   | 0.035049   |   0.0 |  9.40
Neigh   | 0.085828   | 0.08675    | 0.087673   |   0.3 | 23.28
Comm    | 0.05562    | 0.05851    | 0.061399   |   1.2 | 15.70
Output  | 0.0010102  | 0.0011746  | 0.0013391  |   0.5 |  0.32
Modify  | 0.029008   | 0.02926    | 0.029512   |   0.1 |  7.85
Other   |            | 0.02159    |            |       |  5.79

Nlocal:          180.5 ave         181 max         180 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost:          166.5 ave         170 max         163 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs:         1628.5 ave        1652 max        1605 min
Histogram: 1 0 0 0 0 0 0 0 0 1

Total # of neighbors = 3257
Ave neighs/atom = 9.0221607
Ave special neighs/atom = 5.6177285
Neighbor list builds = 1208
Dangerous builds = 0
Total wall time: 0:00:00
